Automated Payroll for Kenyan Schools
Process staff salaries with confidence. Elimika automatically calculates PAYE, NSSF (Phase 4), SHIF, Housing Levy, and HELB deductions using the latest 2025/2026 statutory rates from KRA, NSSF, and the Social Health Authority. Generate payslips, P9 forms, and remittance reports in minutes.
Payroll Module
Statutory Deductions
Updated for 2025/2026 statutory rates
Statutory Deductions — Automatically Calculated
Elimika stays current with all Kenyan statutory deduction rates. Every payroll run automatically calculates the correct amounts for PAYE, NSSF, SHIF, Housing Levy, and HELB based on each employee's gross earnings.
Kenya Revenue Authority (KRA) — Filed via iTax by 9th of following month
PAYE is the income tax deducted from employees' salaries based on progressive tax bands. Elimika calculates taxable income after subtracting tax-exempt allowances and pension contributions, then applies the correct band rates. The KES 2,400 monthly personal relief and any applicable insurance relief are automatically factored in.
2025/2026 PAYE Tax Bands
| Monthly Taxable Income (KES) | Tax Rate |
|---|---|
| 0 – 24,000 | 10% |
| 24,001 – 32,333 | 25% |
| Over 32,333 | 30% |
Personal Relief
KES 2,400 per month (KES 28,800 per year) is automatically deducted from the calculated tax. Insurance relief of 15% of premiums paid (max KES 5,000/month) is also supported where applicable.
Phase 4 Rates — Effective February 2026
The National Social Security Fund Act mandates a phased increase in contribution rates over four years. From February 2026 (Phase 4), both employee and employer contribute 6% of pensionable earnings, up to a combined ceiling of KES 108,000. Contributions are split into two tiers: Tier I funds must go to the NSSF Trust Fund, while Tier II funds can be directed to NSSF or an approved private pension scheme.
NSSF Phase 4 Contribution Structure (Feb 2026)
| Tier | Pensionable Earnings | Rate | Max (Employee) | Max (Employer) | Destination |
|---|---|---|---|---|---|
| Tier I | Up to KES 9,000 | 6% | KES 540 | KES 540 | Must go to NSSF Trust Fund |
| Tier II | KES 9,001 – 108,000 | 6% | KES 5,940 | KES 5,940 | NSSF or approved private pension scheme |
| Total Maximum | Up to KES 108,000 | 6% | KES 6,480 | KES 6,480 | Per month (Phase 4, from Feb 2026) |
Social Health Authority (SHA)
SHIF replaced the National Hospital Insurance Fund (NHIF) effective October 2024 under the Social Health Authority. Unlike the old NHIF fixed bands, SHIF is calculated as a percentage of gross salary, making it proportional to income.
Percentage of gross salary
Floor for low-income earners
Applies to full gross salary
Covers inpatient, outpatient, emergency, maternity, and chronic care. Replaces NHIF from Oct 2024.
National Housing Corporation
The Affordable Housing Levy is a mandatory payroll deduction established under the Affordable Housing Act. Both the employer and employee contribute towards Kenya's affordable housing program.
Deducted from gross salary
Matched contribution by employer
Remitted monthly to the Housing Fund
Elimika tracks both employee and employer portions and generates the combined remittance report for the Housing Fund portal.
HELB (Higher Education Loans Board)
For employees with outstanding HELB loans, Elimika supports variable monthly deductions typically ranging from KES 1,500 to KES 3,000 per month, depending on the loan balance and repayment plan. The deduction amount is configured per employee and included on payslips and the HELB deduction schedule.
Staff Payslip
February 2026
Deductions
Professional PDF Payslips
Generate clear, professional payslips for every staff member with a single click. Each payslip shows a complete breakdown of the employee's earnings, allowances, all statutory deductions, and the final net pay — giving staff full transparency into their compensation.
Payslips are branded with your school logo and can be downloaded as PDF files, printed for distribution, or shared electronically. The system maintains a complete payslip history for every employee, making it easy to reference past months for audits or employee inquiries.
Statutory Reports & Tax Certificates
Generate all the reports your school needs for statutory compliance — from monthly remittance schedules to annual P9 certificates for KRA filing.
P9 Tax Deduction Certificate
Annual tax certificate for each employee showing total earnings, PAYE deducted, and personal relief claimed. Required for KRA annual tax returns via iTax.
NSSF Monthly Report
Monthly schedule of all NSSF Tier I and Tier II contributions per employee, ready for submission through the NSSF online portal.
SHIF Remittance Report
Monthly Social Health Insurance Fund contributions schedule showing 2.75% deductions per employee, formatted for SHA eCitizen submission.
Housing Levy Report
Monthly report of Affordable Housing Levy deductions (1.5% employee + 1.5% employer) for submission through the Housing Fund portal.
HELB Deduction Schedule
Monthly schedule of HELB loan repayment deductions for employees with outstanding higher education loans.
Payroll Summary
Comprehensive monthly summary showing total gross pay, all deductions broken down by category, net pay, and employer contributions.
Allowances, Advances & Bonus Management
Beyond basic salary and statutory deductions, Elimika manages the full range of staff compensation. Configure multiple allowance types per employee, process salary advances with automatic recovery, and manage end-of-year bonuses — all integrated into the payroll calculation engine.
House Allowance
Monthly housing benefit, taxable under PAYE
Transport Allowance
Commuter transport reimbursement
Hardship Allowance
For staff in remote or hardship areas
Responsibility Allowance
For Head of Department, class teachers
Leave Allowance
Annual leave encashment benefit
Medical Allowance
Additional health cover beyond SHIF
Process salary advances for staff with automatic deduction recovery over subsequent pay periods. Set the advance amount, choose the number of installments for recovery, and the system handles the rest.
Process end-of-year bonuses, performance incentives, or ad-hoc payments with correct tax treatment. Bonuses are taxed as lump sums under the applicable PAYE band, and the system calculates the net amount automatically.
Bank Payment Files
Generate formatted payment files for bulk salary transfers through your school's bank.
Run Payroll
Process the monthly payroll with all deductions automatically calculated
Generate File
Export the bank payment file in CSV or the format required by your bank
Upload to Bank
Upload the file to your bank's online portal for bulk salary disbursement
Payment files compatible with all major Kenyan banks
Frequently Asked Questions
Common questions about Elimika's payroll management features.
Automate Your School Payroll
Stop calculating statutory deductions manually. Let Elimika handle PAYE, NSSF, SHIF, and Housing Levy with the correct 2025/2026 rates — every month, automatically. Generate payslips and P9 forms in minutes.
Free to get started. No credit card required. Free training included.